Tuesday, November 24, 2015

Databasing nanomaterials: substance APIs

Cell uptake of gold nanoparticles
in human cells. Source. CC-BY 4.0
Nanomaterials are quite interesting from a science perspective: first, they are materials and not so well-defined as such. The can best be described as a distribution of similar nanoparticles. That is, unlike small compounds, which we commonly describe as pure materials. Nanomaterials have a size distribution, surface differences, etc. But akin the QSAR paradigm, because they are similar enough, we can expect similar interaction effects, and thus treat them as the same. A nanomaterials is basically a large collection of similar nanoparticles.

Until the start interacting, of course. Cell membrane penetration is studies at a single nanoparticle level, and they make interesting pictures of that (see top left). Or when we do computation. Then too, we typically study a single materials. On the other hand, many nanosafety studies work with the materials, at a certain dosage. Study cell death, transcriptional changes, etc, when the materials is brought into contact with some biosample.

The synthesis is equally interesting. Because of the nature of many manufacturing processes (and the literature synthesizing new materials is enormous), it is typically not well understood what the nanomaterial or even nanoparticle looks like. This is overcome by stydying the bulk properties, and report some physicochemical properties, like the size distribution, with methods like DLS and TEM. The field just lacks the equivalent of what NMR is for (small) (organic) compounds.

Now, try capturing this in a unified database. That's exactly what eNanoMapper is doing. And with a modern approach. It's a database project, not a website proejct. We develop APIs and test all aspects of the database extensively using test data. Of course, using the API we can easily create websites (there currently are JavaScript and R client libraries), and we have done so at It's great to be working with so many great domain specialists who get things done!

There is a lot to write and discuss about this, but end now by just pointing you to our recent paper outlining much of the cheminformatics of this new nanosafety database solution.

Of course, we study in our group the nanosafety and nanoresponse (think nanomedicine) at a systems biology level. So, here's the obligatory screenshot of work of one of of interns (Stan van Roij). Not fully integrated with the database yet, though.

Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafstr√∂m, R., Hardy, B., Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D., Willighagen, E., Jul. 2015. The eNanoMapper database for nanomaterial safety information. Beilstein Journal of Nanotechnology 6, 1609-1634.